Cersei plots to shrink the power of House Tyrell, which has gained considerable influence over the Iron Throne due to their military support at the Battle of the Blackwater and Margaery Tyrell's marriage to KingJoffrey I and later Tommen I after Joffrey's death. After the Sparrows have the High Septon partake in a walk of atonement, Cersei names the High Sparrow as the new High Septon in her son Tommen's name. She also reestablishes the Faith Militant, allowing the Sparrows to deliver their version of justice across the realm "in the eyes of the Seven". Soon after, Cersei informs the High Sparrow of a "great sinner in their very midst": her formerly betrothed, SerLoras Tyrell. Loras is arrested by the Faith Militant; later, a hearing is held for Loras, which is attended by King Tommen, Cersei, Queen Margaery, and Olenna Tyrell, grandmother of Loras and Margaery. Accused of homosexuality, Loras denies he ever slept with Renly Baratheon (in reality, his deceased lover) or any other men, and Margaery says the same when she is called to testify on Loras's behalf. However, Olyvar, Loras's former squire who was by then secretly in the employment of Petyr Baelish, testified that he slept with Loras and Margaery walked in on them once, unsurprised and undisturbed by what they were doing. He proves this by describing a birthmark on Loras's upper thigh. Both Loras and Margaery are imprisoned for lying before the gods.

As expected, Cersei is pleased with these results as they reduce House Tyrell's power over the throne. Her plan backfires, however, and she is later imprisoned by the Sparrows herself after her cousin Lancel Lannister (now "Brother Lancel") confesses to having slept with her. Cersei is accused of multiple crimes, including murdering King Robert I and committing incest; however, she only confesses to adultery. For this confession, she is allowed to return to the Red Keep to reunite with her son, but to do so, she is forced to undertake a walk of atonement from the Great Sept of Baelor to the Red Keep.

Cersei's Revenge

Cersei begins to plot her revenge against the Sparrows. As she has yet to confess to all of her crimes, a formal trial is to be held for her. Cersei intends to use the revived Gregor Clegane, her new Kingsguard, to serve as her champion in a trial by combat. However, she also wants to smooth relations between the Lannisters and the Tyrells. She and Jaime both convince Olenna Tyrell to allow the Tyrell army to march into King's Landing to prevent Margaery Tyrell from having to participate in her own walk of atonement, and convince Kevan to keep the gates open, using his son Lancel as a point of persuasion.

Shortly before Queen Margaery's walk of atonement, the Tyrell army arrives with Lord Mace Tyrell and Ser Jaime Lannister of the Kingsguard at its command. However, the High Sparrow declares that Margaery's punishment has been revoked for her help in forming a new holy alliance between the Faith of the Seven and the Iron Throne, as King Tommen emerges from the Sept as a new convert. For "attacking the Faith," Tommen dismisses Jaime Lannister from the Kingsguard and orders him to besiege Riverrun for House Frey in the Riverlands, which has been retaken by Ser Brynden Tully "the Blackfish". Though Jaime is concerned for Cersei, she reassures him that the Mountain will defend her in her trial by combat.

Cersei's plan is thwarted, however, when after conferring with the High Sparrow, King Tommen abolishes trial by combat across the Seven Kingdoms, after announcing the date for the trials of Ser Loras and Cersei. Seeing no other option, Qyburn informs Cersei that his "little birds" have confirmed a rumor.

The Destruction

Margaery gives a final look to the High Sparrow, signaling that he has doomed them all.

On the day of the trials of Loras and Cersei, Cersei fails to appear at the Great Sept. Having learned of the caches of wildfire that were placed in the tunnels beneath the Sept (by the orders of the Mad King during Robert's Rebellion), she plans to set them alight and destroy the Sept, subsequently killing the High Sparrow and the rest of the Sparrows. Three burning candles are placed in a pool of wildfire, the flames getting closer to the extremely flammable substance as the candles melt. By the time Loras's trial has ended, Queen Margaery realizes that something is wrong, as neither Cersei nor Tommen have yet arrived. She tries to leave the Sept, along with her brother, father, and the rest of the assembly, but the Sparrows prevent them from doing so, as the High Sparrow dismisses her concerns, and insists that the trial must continue. The wildfire plot is discovered by Brother Lancel after he is led into the tunnels and severely injured by one of Qyburn's "little birds". His injury keeps him from getting to the candles in time, and he is the first to be killed as the pool ignites, starting a chain reaction.

Dozens of barrels of wildfire ignite and explode, flooding the tunnels with fire. As Margaery locks eyes with the High Sparrow for the last time, the fire punches through the seven-pointed star mosaic floor directly where the High Sparrow was standing, killing him instantly. The statues of the Seven crack and shatter under the force of the explosion and the flames spread everywhere, killing the entire assembly.

The High Sparrow is engulfed in wildfire.

The explosion builds in intensity, blowing out the windows and shattering the stonework of the building. Civilians gathered outside are incinerated as the shockwave spreads the flames outwards and obliterates all structures within a hundred meters of the Great Sept. A bell from one of the Sept's towers is flung from the structure and takes a chunk out of a building before crashing into the street below, killing at least one man before flames engulf the area. As smoke and the screams of the terrified populace fill the air, Cersei looks on from her chamber in the Red Keep with great satisfaction, while Tommen, who was forced to remain in the Red Keep by Ser Gregor, watches on with shock and horror as the shattered remains of the once magnificent Sept crumble to the ground.

Aftermath

The destruction of the Great Sept had many far-reaching consequences. House Lannister has been pushed further to the brink of collapse with the deaths of Ser Kevan Lannister and his sole remaining son, Lancel, in the explosion. The deaths of Mace Tyrell and Grand Maester Pycelle wiped out the remainder of the Small Council that were not Cersei's allies or sycophants. In addition, the entire leadership of the Faith of the Seven has been destroyed, including the High Sparrow and the Faith Militant, crippling the church's power in the realm. A large number of the royal court and minor nobles or representatives of lesser or vassal Houses were also killed, as well as hundreds of innocent smallfolk caught in the blast or killed by debris. Finally, King Tommen was driven to commit suicide out of grief from the deaths of his wife, extended family, and so many innocents. With his death, Cersei is crowned as the first Queen of the Andals and the First Men since Rhaenyra Targaryen. Jaime returns to King's Landing just as Cersei is taking the throne. His expression is grim as he watches his sister become the newly-seated Queen. King Tommen's death also marks the official extinction of House Baratheon, even though he wasn't a true Baratheon.

The most dramatic consequence, however, is that House Tyrell, the only participating Great House to have suffered no major losses during the War of the Five Kings (House Arryn remained neutral), has been nearly eradicated with the deaths of Margaery, Mace, and Loras, prompting an enraged and devastated Lady Olenna Tyrell (a Redwyne by birth) to withdraw the Reach from the sovereignty of the Iron Throne. Seeking vengeance on Cersei, Olenna accepts an offer of alliance with the similarly-wounded de facto ruler of Dorne, Ellaria Sand, who reveals that after hearing of Daenerys Targaryen's recent alliance with Theon and Yara Greyjoy, has been working with Varys in preparing for the return of House Targaryen to the Seven Kingdoms. When Daenerys and her armada set sail for Westeros, ships of Dorne and House Tyrell can be glimpsed amongst the black Targaryen sails.

Cersei's actions, at first, most likely doomed her reign before it even began, with House Arryn (under Petyr Baelish) allied with the resurgent Kingdom of the North, the deaths of Walder Frey and his sons have left House Frey without a Lord or male heir, and Dorne and House Tyrell aligned with Daenerys's already massive forces. As Jaime has pointed out, Cersei rules three of the Seven Kingdoms at most. Making matters worse, Cersei is too arrogant to understand her predicament. She even has the audacity to proclaim herself the Protector of the Seven Kingdoms to her surviving subjects, totally ignoring the fact that she just destroyed half her own city with wildfire and murdered thousands of people whose only crime was to oppose or dislike her or who were simply unlucky enough to be in the blast radius. Cersei also cannot rely on any religious support, having wiped out the entire Faith of the Seven's power and administration and also having broken every rule in the book.

Though she manages to turn her situation around by getting Euron Greyjoy, with his navy destroying most of Daenerys's fleet, capturing her allies Ellaria Sand and Yara Greyjoy and destroying the Unsullied fleet at the Siege of Casterly Rock, and Randyll Tarly, whose army in conjunction with hers sacks Highgarden, removes Lady Olenna Tyrell as a threat and seizes its gold reserves to pay the Iron Bank of Braavos so they support her claim, her situation is still shaky. The Dornish armies are still intact, as are the Reach's (those who are not Tarly bannermen or who died defending Highgarden) though both are leaderless, Daenerys still has a decent fleet and her three dragons who are formidable on their own, and the North and the Vale are still in rebellion though preparing for the war with the dead. Also, the Iron Bank of Braavos have made it clear they will only support her once they are paid; though the gold from Highgarden has made it, more is needed, and the Lannister army has been ambushed by a Dothraki battalion led by Daenerys with aerial support from Drogon, likely preventing more gold from reaching King's Landing.

And finally, the most pressing matter which she as usual completely ignores even though it has been bearing down and been mentioned countless times; Winter has come. King's Landing does not have enough food for its people to survive a long winter, as the Tyrells ceased supplying the capital after their heirs were murdered and the other Kingdoms will be consolidating their own resources to last it. And of course, the threat of the White Walkers looms, and while she is aware of this, she intends to violate her vow to support Daenerys and Jon Snow in the Great War in the hope that they will be weakened enough for her to defeat them, leading Jaime, the commander of the Lannister forces, to abandon her; if Daenerys and Jon do defeat the White Walkers, they will be well aware that Cersei has betrayed them and likely unwilling to trust another one of her truces.

In the books

In A Song of Ice and Fire novels there is no parallel scene, because the TV show's storyline has surpassed them.

By the end of the last book, since Cersei's walk of atonement, she has been stripped of all power and influence, confined to her rooms and under guard all the time. She is forbidden to receive visitors without Kevan's permission, unable to walk freely and intimidate people as she did in the show; whatever plots she has in mind, at the moment, she is unable to carry them out.

Mace Tyrell, Queen Margaery, Lancel, the High Sparrow, the Faith Militant, and King Tommen are still alive.

Loras is lying near death, but it is not Cersei's fault; he volunteered to resolve the siege of Dragonstone, and was subsequently gravely injured as a result of his rashness, just as Cersei had hoped.

Margaery and her cousins were released to Randyll Tarly's custody, since the case against them is weak, and the witnesses Cersei arranged against them are proved to be false.

Kevan and Pycelle have been murdered, but Cersei and Qyburn had nothing to do with it; Varys killed them because they had been acting to undo Cersei's mistakes and restore the peace. As Kevan dies, Varys explains that his death will undermine the alliance between the Lannisters and Tyrells and open the way for a Targaryen (who is more than likely not going to appear in the show, as it is not Daenerys or Jon Snow) to retake the Iron Throne.

The only time in the novels where Cersei has used wildfire is in A Feast for Crows, where she burns the Tower of the Hand shortly after Tywin's funeral. She announces her intention to do that in advance, and no one is harmed.